Antigen

Antigen Class

TFs and others

Antigen

Rxra

Cell type

Cell type Class

Liver

Cell type

Liver

MeSH Description

A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Sample

source_name

RXR_Male_Vehicle_27hr_Liver

strain

CD-1 (Charles River)

Sex

male

age

8 weeks

treatment

Vehicle (1% DMSO in corn oil)_ 27 h

tissue

liver

chip antibody

RXRa (Santa-Cruz Biotechnology #SC-553)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chromatin was extracted from frozen liver tissue from each of the individual livers per group. Crosslinking was achieved by adding formaldehyde to a final concentration of 1% for 5 min at room temperature. ChIP was performed using the following ChIP-validated antibodies: RXRa (Santa-Cruz Biotechnology #SC-553), CEBPa (Santa-Cruz Biotechnology #SC-61), CEBPb (Santa-Cruz Biotechnology #SC-150). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep kit for Illumina (NEB, catalog no. E7645) according to the manufacturer's instructions. NEBNext Multiplex Oligos for Illumina (NEB, Set 1; catalog no. E7335, NEB, Set 2; catalog no. E7500) were used for multiplexing. Samples marked input control correspond to sequencing libraries from sonicated chromatin that was not subject to ChIP.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

21249678

Reads aligned (%)

96.9

Duplicates removed (%)

13.2

Number of peaks

12867 (qval < 1E-05)

mm9

Number of total reads

21249678

Reads aligned (%)

96.7

Duplicates removed (%)

13.9

Number of peaks

12850 (qval < 1E-05)